The Clear Bell reappears in Pokémon HeartGold and SoulSilver, where it is instead received from the Kimono Girls in HeartGold only. In SoulSilver, its purpose is replaced by the Tidal Bell. While Suicune takes a particular interest in the player once more, it is not involved with the Clear Bell whatsoever, with the item combining with the power of the Rainbow Wing and the dance of the Kimono Girls to summon Ho-Oh to the Bell Tower. Much like how the Tidal Bell is not required in HeartGold to encounter Lugia, with the Pokémon appearing with just the Silver Wing obtained in Pewter City, the Clear Bell is not required in SoulSilver to encounter Ho-Oh.

In the anime

A Crystal Bell in anime

In the anime, the connection between the Crystal Bells and Bell Tower was made explicitly clear in For Ho-Oh the Bells Toll!, when Ash and his friends returned to Ecruteak on their way to Mahogany Town. Jessie, James, and Meowth stole some of the bells from the Bell Tower, intending to summon legendary Pokémon with them. However, their thievery was detected by the Pokémon of the area, who proceeded to ensnare them in webbing, apprehending them long before Morty, along with Ash, Misty, Brock, and Eusine, caught up.

The Crystal Bells are unable to be rung by human hands alone, as Jessie proved, though they will, according to legend, ring on their own when Ho-Oh approaches.

In the manga

In the Pokémon Adventures manga

The Clear Bell was obtained by the Masked Man with the hopes that his new minions would be able to track down and stall Suicune with it. However, they failed, and Eusine got his hands on it instead. With its ability of allowing the holder to freely bypass Suicune's crystal walls, he proved invaluable in the final battle against the villain by rescuing Suicune and its Trainer both when they were injured by Gastly. Despite this, the legendary Pokémon chose Crystal as its new partner instead, much to the Eusine's disappointment.

Trivia

Though the Japanese and English names of the item imply that the bells should at least be somewhat transparent, the Generation IV sprite of the item is not clear at all, nor even blue, the color of Pokémon Crystal's cartridge, except when it is being used to summon Ho-Oh, in which it shines brightly with a bluish-white glow as if it became clear.